Transcript owen unit 2 biochem

Matter
Every
thing in the
universe is made up of
matter
Changes in matter are
essential for all life
processes
Composition of Matter

Matter = anything that occupies space & has
mass.

Mass = the quantity of matter an object has.

Weight = the pull of gravity (less weight on the
moon).
Atom
Fundamental
unit of
matter
Discovered by
Democritus 3000yrs ago
Proved by John Daltons
in his Atomic theory

Proton :Positive charge ( in nucleus) ( id Number
of element)

Neutron: neutral charge ( in nucleus)

Electron :negative charge ( outside nucleus)

Protons + neutrons = atomic weight

Most of mass of atom is in nucleus

Most space of atom is electron cloud
Wolverine: made of protons, neutrons,
electrons
A Wolverine = Protons, Neutrons, & Electrons



All P, N, and E are the
same.
Yet, the number of P,
N, and E in an atom
changes its
properties.
Also, the type and
number of elements
in a molecule also
changes the
properties of the
substance.
Element

A substance which cannot be decomposed into
simpler substances by chemical reactions

Composed of building blocks called Atoms

92 naturally occurring elements

About 98% of an organisms mass is composed of
just 6 elements:


Carbon
Oxygen
Hydrogen
Nitrogen
Calcium
Phosporus
Isomers
Isomers – compounds with the same formula but
different forms.
Glucose is the main source of energy for cells.
Fructose is found in fruits and is the sweetest
of the monosaccharides.
Galactose is found in milk.

Chemical compound : consists of 2 or more
different elements combined in a fixed ration ex
H2O

Chemical formula: short hand method for
describing chemical composition of a compound

Chemical reaction: when atoms combine or
break apart from other atoms
Molecules

Molecule is the simplest
part of a substance
retaining all of the properties and can exist
in free state.

Examples are sugar C6H12O6, water H2O, oxygenO2, hydrogen H2,
etc.

C6H12O6 and H2O are also compounds.

O2 and H2 are not compounds.
Bonds:

Chemical bonds : forces of attraction due to
outer shell electrons
Types of Bonds:

1. Covalent bonds

2. Ionic bonds

3. Hydrogen bonds

4. Van Der Waals forces
5. Hydrophobic interactions
Ionic Bonds


Gaining and losing electrons ( metal
and nonmetal)
Ionic compounds in water tend to
dissociate into free ions for other
chemical reaction.
Dissolved ionic compounds are in all aqueous
solutions of living things, and are critical to
normal operation of body/cell systems
 (Example: Na and Cl ions are vital to nerve
and muscle cell functions)

covalent bond

The covalent bond involves a sharing of
electrons between two nonmetals.

The sharing of electrons can be an equal sharing (
nonpolar), or an unequal sharing (polar)

Polarity = uneven pattern of electrical charge in
molecules such as water.
- Water’s biological functions stem from its polar chemical
structure.
- The covalent bond sharing of electrons between O and H is not
equal.
- Oxygen has 8 positive protons to attract the electrons closer than
hydrogen’s one.
- - The polar structure makes water a very effective solvent, for
other polar substances.
(sugars, proteins, & ionic compounds like NaCl)
-
Hydrogen Bonding

the type of bond attracting water molecules to
one another.

Weak bonds that gain strength in numbers
Ionic Bonding
http://nutrition.jbpub.com/images/images/3.3.gif
Van der Waals Forces:

Caused by temporary shifts in charges due to
electron interactions

Molecules must be very close

Important in enzymatic reaction
Hydrophobic interactions
Means
water fearing
Very weak bonds
formed between
molecules that are
insoluble in water
Chemical Reactions

NaI + KCl -------- NaCl + KI

Reactants
products
Types:

1. Syntheis Rxn (anabolic): combination of 2 or
more atoms to form a new molecule

Ex 2H2 +O2-----2H2O
Chemical Reactions

2. Decomposition reaction (catabolic rxn):
opposite of synthesis rxn

Ex 2H2O ------ 2H2 + O2

3. Exchange reaction: A combination of both
types of bonds both broken and formed

Ex NaI + KCl -------- NaCl + KI
Mixtures

The combined substances combined keep their
original chemical properties

Types:

1. solution: combination of solvent and solute

Solvent: material in greater amount

Solute: material in lesser amount

2. Suspension: The material mixed in a suspension
will settle out with time. Ex. Salt water

3. colloid: mixtures in which like solutions, particles
don’t settle out over time

Ex warm water and geletin powder
Acids and bases
Acids:

substances which when
dissolved are hydrogen
donors (proton donors)
Base:

substances which when
dissolved are hydrogen
acceptors (proton
acceptors)

Also called alkaline
Acids and bases

Acid Properties:
Sour taste
2. Contain
hydrogen
3. Turn litmus
paper red
4. React wit base
to form salt
and water
1.

Base Properties:
1.
bitter taste
2.
Contain OH
3.
Turn litmus paper blue
4.
slippery
PH Scale

Ranges from 0 t0 14

Less than 7 = acid

7= neutral
greater than 7= base
Beware of the DIRECTION of the scale on different charts

Litmus paper = a chemical indicator used to measure or test pH
levels (changes color).

Buffers = chemical substances that neutralize small amounts of
either an acid or a base added to a solution. Enzymes can only
function within a very narrow range of pH, so buffers are used in
living systems to control pH.
Water

Aqueous (Water) Solutions are crucial for the chemical
reactions of living things.

Earth’s Distance from the Sun is perfectly designed for water.

Closer to the sun and water would boil off of earth

Farther away and water on Earth would freeze.
The Water of Life
Water
Properites of water
Hydrogen Bonding = the type of bond
attracting
water molecules to one
another.
- The positive region of one water
molecule is attracted to the negative of
another.
- It is a weak bond, that’s easily broken,
yet strong
enough to produce two
special forces:
*



Cohesion = attractive force between particles of
the same kind (water to water).(Ex: thin “skin” on
the surface of water that spiders walk upon)
Adhesion = attractive force between unlike
substances, like capillarity in plants.
Capillarity allows water to move upward through
narrow tubes like plants. (The water molecules
are attracted by the sides of the tube and pulled
upward.)

Temperature Moderation:
Water helps maintain homeostasis!


Water changes temperature slowly, since it must gain or lose a large
amount of energy.

When heated, most of the initial thermal energy simply breaks the
hydrogen bonds.

Only after these bonds are broken do the molecules increase in
motion and temperature.
Human body is 70% water, which helps keep us from getting too
hot or cold.
Water has the highest specific heat
of any common substance, 1
calorie/gm °C = 4.186 J/gm °C.
This provides stability of
temperature for land masses
surrounded by water, provides
stability for the temperature of the
human body, makes it an effective
cooling agent, and many other
benefits. The high heat of
vaporization of water makes it an
effective coolant for the human
body via evaporation of
perspiration, extending the range
of temperatures in which humans
can exist.
Carbon Compounds
Organic Compounds = contain carbon atoms
covalently bonded to other elements.
- A carbon atom has four electrons in the outer
energy level.
- So it can form four covalent bonds with other
elements.
- They form either straight chains, branched chains,
or rings.
- The covalent bonds can be the sharing of single,
double, or triple pairs of electrons.
* This is shown by corresponding lines
(-) (=) in chemical shorthand.
How Important is Energy ?
- on average a person. . .

Can live about 30-40 days without food.

Can live about 3-4 days without water.

Can live about 3-4 minutes w/o oxygen.

Can live about 3-4 seconds w/o energy (ATP).
Energy Currency:
* Life processes require a constant supply of energy.
* The energy is available to cells in the form of chemical
energy in certain compounds.
ATP
*
(Adenosine Triphosphate) is a very important energy
compound for cells.
* When the covalent bond of the third phosphate
group (-PO4-) is broken, it releases much more
energy than was required to break the bond. This
energy is used by the cell to drive chemical
reactions for the cell to function.
The hydrolysis of ATP yields ADP
(Adenosine Diphosphate) (“Di” = two phosphates)
ATP – Adenosine
Triphosphate
Molecules of Life

Four main classes of essential organic compounds.
Carbohydrates
Lipids
Proteins
Nucleic
acids.

All are built from C, H, O, yet each compound has unique
properties.

The atoms merely occur in different ratios.
1. Carbohydrates
1. Carbohydrates = organic compounds of C, H, O.
 The
ratio is about two H per one O, while the C atoms
vary.
 Carbohydrates exists as Monosaccharides,
disaccharides, or polysaccharides.

a. Monosaccharides = a monomer of a
carbohydrate. (a simple sugar)
 Most
common are glucose, fructose, and galactose.
 They all have the same formula C6H1206, yet each has a
different structure, which determine slightly different
properties of the compounds.
Carbohydrates continued
b. Disaccharides = two monosaccharides
combined by a condensation reaction.
 * Table sugar is a double sugar
composed of fructose and glucose.
 c. Polysaccharide = complex molecule
composed of three or more
monosaccharides.
 Glycogen = a polysaccharide used by
animals to store glucose.
 It consist of 100’s of glucose molecules
strung in a complex branched chain.
 Starch = polysaccharide used by plants to
store glucose.

Disaccharide
Proteins

Proteins = organic, macromolecule compounds
composed mainly of C, H, O, N.
Amino Acids = the monomer building blocks of proteins.
 There are 20 basic amino acids, which all share a basic
structure.
 Each w/ central C atom, covalently bonded to four
other atoms (or functional groups).

1. Single Hydrogen atom
2. Carboxyl group – COOH
3. Amino Group –NH2
4. R Group, which is the main difference among the different
amino acids.
- The R group can be as simple as a single hydrogen or more
complex.
- The different R group gives it a different shape, which allows it
to perform different roles.
Amino Acids have:
Central Carbon & Four Functional
Groups
2. Proteins continued

Dipeptide = two amino acids form a covalent bond in a
condensation reaction.

Peptide Bond = the covalent bond between the amino acids.
Polypeptide = many amino acids bonded together one at a
time.
 Protein = one or more polypeptides.

Some proteins have hundreds of amino acids, bent and folded
upon themselves, due to hydrogen bonding among the amino
acids.
 Protein shape determines its function, and the shape can
changed by conditions.
 (Heat turns egg white from clear and runny, to stiff and opaque.)


* Enzymes (most are proteins) Enzyme reactions depend on
a physical fit between the enzyme molecule and the
substrate (the reactant being catalyzed). The linkage with
an enzyme probably causes the weakening of chemical
bonds in the substrate, which reduces the activation energy.

Change in temperature or pH of the solution affects the enzyme’s
effectiveness.
Dipeptide
Enzyme-Substrate Model
Substrate
Products
Enzyme
3. Lipids

3. Lipids = large non-polar organic molecules that do not
dissolve in water.

Lipids store more energy than other organic molecules, due to
many C-H bonds
Fatty Acids = unbranched carbon chains that make up most lipids.

The ends of the fatty acid molecule have very different
properties.

The carboxyl end (-COOH) is polar and attracted to water (hydrophilic).

The hydrocarbon end (C-H) is nonpolar and called hydrophobic.

Unsaturated lipids – have one or more pairs of carbon atoms
joined by double bonds.

Saturated lipids have no double bonds between their carbon
atoms.
Fatty Acid
Complex Lipids:

Complex Lipids: three classes of lipids important to
living organisms
a.
b.
Triglycerides = 3 molecules of fatty acid joined to 1 of the
alcohol glycerol.
Phospholipids = have 2 rather than 3 fatty acids joined by the
glycerol.
- Cell membranes are composed of a bilayer made from a
double row of phospholipids, arranged with their hydrophobic
“tails” facing each other. Since lipids do not dissolve in water, the
membrane is a barrier between the inside and outside of the cell.
c. Wax = a type of structural lipid, consisting of a long fatty-acid
chain joined to a long alcohol chain.
** Steroids = lipids that are NOT composed of fatty
acids, but of four fused carbon rings.


Each carbon ring has various function groups attached to it.
Many animal hormones, like testosterone are steroids.
4. Nucleic Acids
Nucleic Acids = very large and complex molecules that store
information in the cell.
 Similar to a computer’s binary code of zeros and ones.
 Nucleic acids use four compounds to store hereditary
information.
 The order of arrangement of these four determines the code.
 DNA = Deoxyribonucleic Acid, contains the information for all cell
activities, including cell division. (Designed Not Accidental)
 RNA = Ribonucleic Acid, stores and transfers information for
making proteins.
 Both DNA and RNA are polymers, composed of thousands of
linked monomers.
 Nucleotides are the monomers. Each is composed of three main
components:
a.
b.
c.
Phosphate group
Five-carbon sugar
Ring-shaped nitrogen base
DNA
= Deoxyribonucleic
Acid, contains the
information for all cell
activities, including cell
division.

Nucleotides are the monomers. Each is
composed of three main components:
a.
Phosphate group
b.
Five-carbon sugar
c.
Ring-shaped nitrogen base
Nucleotide
Phosphate
Nitrogen Base
Deoxyribose (sugar)